Cleaning of PES membranes after ultrafiltration of skim milk is still often performed at industrial scale with a formulated alkaline first step followed by a nitric acid step. This cleaning mode gives sufficiently satisfactory results in terms of water flux recovery but cannot prevent a progressive decline of production flux over time. The analysis of the deposit on the membrane by FTIR-ATR highlights the nature of the irreversible fouling, exclusively made of proteins, and the real cleaning efficiency. Sodium hydroxides alone allows up to 24% of protein removal which is in good agreement with the water flux recovery after this treatment. Nevertheless, the amount of protein remains exactly the same after nitric acid treatment whereas the flux significantly grows. This flux increase without any protein removal is strongly dependent on the proteins amount on the membrane at the start of nitric acid step. This phenomenon is not observed with HCl, but it seems not totally specific from HNO3 as the use of H3PO4 in particular leads also to similar results. The specific adsorption of oxoanions on proteins at acid pH that will change the hydrophobicity of the deposit is suspected. The nitric acid step can be suppressed as it is useless and misleads on the real efficiency of the overall cleaning. (C) 2012 Elsevier B.V. All rights reserved.